merge build.xml

build.xml

@@ -17,9 +17,9 @@
 	<property name="libBeast2" location="${beast2path}/lib" />
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
-    <property name="beastlabsclasspath" location="../BEASTLabs/build" />
+    <!--<property name="beastlabsclasspath" location="../BEASTLabs/build" />-->
     <property name="bdskyclasspath" location="../bdsky/build" />
-    <property name="masterclasspath" location="../MASTER/build" />
+    <!--<property name="masterclasspath" location="../MASTER/build" />-->
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
 
     <import file="${beast2path}/build.xml" />
@@ -37,9 +37,9 @@
 		<fileset dir="${libBeast2}" includes="commons-math3-3.1.1.jar"/>
         <fileset dir="${libBeast2}" includes="antlr-runtime-4.7.jar"/>
         <pathelement path="${beast2classpath}"/>
-        <pathelement path="${beastlabsclasspath}"/>
+        <!--pathelement path="${beastlabsclasspath}"/-->
         <pathelement path="${bdskyclasspath}"/>
-        <pathelement path="${masterclasspath}"/>
+        <!--<pathelement path="${masterclasspath}"/>-->
 	</path>
 
 	<!-- start -->
@@ -89,7 +89,11 @@
 			<include name="beast/**/**" />
 			<!-- compile JUnit test classes -->
 			<include name="test/beast/**" />
+			<include name="test/phylodynamics/**" />
 		</javac>
+		<copy todir="${build}">
+			<fileset dir="${srcphylodynamics}" includes="test/phylodynamics/epidemiology/TestTrajectory.txt" />
+		</copy>
 		<echo message="Successfully compiled." />
 	</target>
 
@@ -153,11 +157,12 @@
 
 			<batchtest fork="yes" todir="${report}">
 				<fileset dir="${srcphylodynamics}">
-                    <include name="test/**/*Test.java"/>                                         
+                    <include name="test/**/*Test.java"/>
+					<exclude name="test/phylodynamics/epidemiology/**/VolzSIRTest.java"/>
 				</fileset>
 				<fileset dir="${srcBeast2}">
                     <include name="test/beast/integration/**/*Test.java"/>                                         
-                    <exclude name="test/beast/integration/**/ResumeTest.java"/>                                         
+                    <exclude name="test/beast/integration/**/ResumeTest.java"/>
 				</fileset>
 			</batchtest>
 		</junit>

examples/BDSIR.xml

@@ -12,7 +12,8 @@
   </tree>
 
 	<BDSIR spec="beast.phylodynamics.BDSIR" id="birthDeath" tree="@tree" dS="@dS" dR="@dR" checkTreeConsistent="false">
-		<parameter name="origin" id="origin" value ="12.7808530307"/> 
+		<!--origin must > tree height(12.485382039003651)-->
+		<parameter name="origin" id="origin" value ="15"/>
 		<parameter name="reproductiveNumber" id="reproductiveNumber" value="2.5" lower="0." upper="10."/>
 		<parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate" value="0.25" lower="0."/>
 		<parameter name="samplingProportion" id="samplingProportion" value="0.10" lower="0." upper="1."/>

src/beast/evolution/tree/coalescent/StochasticCoalescentSkyline.java

@@ -22,7 +22,7 @@ public class StochasticCoalescentSkyline extends TreeDistribution {
     public Input<RealParameter> infectedPopulationInput = new Input<RealParameter>("infectedPopulation", "infected population size at times eventTimes",
             Input.Validate.REQUIRED);
 
-    public Input<RealParameter> transmissionRateInput = new Input<RealParameter>("transmissionRate", "the transmission rate",
+    public Input<RealParameter> transmissionRateInput = new Input<RealParameter>("transmissionRate", "the transmission rate β",
             Input.Validate.REQUIRED);
 
     public Input<RealParameter> eventTimeInput = new Input<RealParameter>("eventTimes", "event times from first infection to present (i.e. in forward time)",

src/beast/phylodynamics/epidemiology/CoalescentSIR.java

@@ -1,6 +1,7 @@
 package beast.phylodynamics.epidemiology;
 
 import beast.core.CalculationNode;
+import beast.core.Description;
 import beast.core.Input;
 import beast.core.Loggable;
 import beast.core.parameter.RealParameter;
@@ -20,6 +21,7 @@
  * @author Alexei Drummond
  * @author Alex Popinga
  */
+@Description("A coalescent approach for SIR model")
 public abstract class CoalescentSIR extends CalculationNode implements Loggable {
 
     public Input<RealParameter> betaParameter = new Input<RealParameter>("beta",

src/beast/phylodynamics/epidemiology/CoalescentSimulator.java

@@ -24,7 +24,7 @@
 @Description("Performs random tree generation for a given site model. ")
 public class CoalescentSimulator extends beast.core.Runnable {
     public Input<PopulationFunction> populationFunctionInput
-            = new Input<PopulationFunction>("populationFunction", "the population function", Input.Validate.REQUIRED);
+            = new Input<PopulationFunction>("populationFunction", "the population size function", Input.Validate.REQUIRED);
     public Input<Integer> ntaxaInput = new Input<Integer>("ntaxa", "the number of taxa", Input.Validate.REQUIRED);
     public Input<Integer> replicatesInput = new Input<Integer>("replicates", "the number of replicates", Input.Validate.REQUIRED);
     public Input<String> outputFileNameInput = new Input<String>(

src/beast/phylodynamics/epidemiology/SIRPopulationFunction.java

@@ -17,7 +17,7 @@
 public class SIRPopulationFunction extends PopulationFunction.Abstract {
 
 
-    public Input<CoalescentSIR> volzSIR = new Input<CoalescentSIR>("volzSIR", "Volz parameters");
+    public Input<CoalescentSIR> volzSIR = new Input<CoalescentSIR>("volzSIR", "Volz parameters for coalescent SIR");
 
     public Input<Boolean> oldMethodInput = new Input<Boolean>(
             "oldMethod",

src/beast/phylodynamics/epidemiology/Volz2009TreeDistribution.java

@@ -21,7 +21,8 @@
 @Description("Calculates the Volz-2009 probability of a beast.tree.")
 public class Volz2009TreeDistribution extends TreeDistribution {
 
-    public Input<DeterministicCoalescentSIR> volzSIRInput = new Input<DeterministicCoalescentSIR>("volzSIR", "Volz parameters", Input.Validate.REQUIRED);
+    public Input<DeterministicCoalescentSIR> volzSIRInput = new Input<DeterministicCoalescentSIR>("volzSIR",
+            "Volz parameters for deterministic coalescent SIR", Input.Validate.REQUIRED);
 
     TreeIntervals intervals;
 

src/test/phylodynamics/epidemiology/VolzSIRTest.java

@@ -9,6 +9,7 @@
 import test.beast.BEASTTestCase;
 
 /**
+ * TODO it seems still in development, excluded in build.xml
  * @author Alexei Drummond
  */
 public class VolzSIRTest extends BEASTTestCase {